15	0	* Method(s) expressed by M and possibly T (details below)
3		* number of (positive) critical values C
0.05  0.02  0.01	* Critical values (have this line only if C > 0)
0  0  1.5	* Generations (have this line only if Temporal is included)
15  0  1	* Methods to have outputs in tabular-format (details below)
1		* 1 for output Confidence Intervals, 0 if none
0		* mating model, 0: random, 1: monogamy (if LD is included)
0		* max individual to be processed per pop, 0 for no limit
0		* Pop. range to run, given in pair. No limit if the first = 0
0		* Loc. ranges to run, given in pairs. No limit if the 1st = 0
myCommon.out	* name for common (main) output file
test1.gen	* this and subsequent lines are for input file names.
test2.txt
test3.gen
*

Either an empty line, or a line starting with an asterisk, will end the list
of input file names. Asterisks are used to mark the end of data for the lines,
they are optional, used to insert comments.

To run Ne2 with input files listed in this file, open a terminal at the
directory containing the executable Ne2, this control file, and all input
files mentioned in this file.
Then issue command line (assuming this file is named "common.txt"):
	  Ne2 c:common.txt	(Windows)
	./Ne2M c:common.txt	(Mac)
	./Ne2L c:common.txt	(Linux)
(preceding the name of this file are two preset key characters:
letter 'c' followed by a colon ':').

General Instructions
--------------------
All input files are run with the same method(s) and options.
The leading lines, up to 10 lines, are for these common settings.
One line less if there is no temporal method (M < 8 on line 1).
One line less if no positive critical values (C = 0 on line 2).
One line less if no Linkage Disequilibrium method (when M is an even number on line 1).
Thus, common settings require 7 to 10 lines.
Then they are followed by the name for the main output file.
Extra output files will be named based on the name of main output.
Subsequent lines are for the names of input files to be run.
Each output file is for outputs of all input files listed here.

Each line can be terminated by a white space (blank or tab) followed by an
asterisk (then comments can be put on the line after the asterisk).
Note that the asterisk should be after a white space,
unless at the line for output file name, where the asterisk will play a role
(see details for line 11 below).


DETAILS
-------
Line numbering assumes positive critical values are desired, and LD, temporal
methods are included.
 
Line 1:  A number M from 1 to 15 to indicate which method(s) to run:
                  M = 1 for Linkage Disequilibrium method (LD),
                  M = 2 for Heterozygote Excess method (Ht),
                  M = 4 for Molecular Coancestry method (Cn),
                  M = 8 for Temporal methods (Tp).

         For multiple methods, M is the sum of the designated method numbers.
         Examples: M = 3 = LD + Ht; M = 9 = LD + Tp.

         A second number T can be entered to indicate which temporal methods
         to run (if temporal is indicated by entry M >= 8). T can be any
         number at least 0.
         * If T = 0, or T is at least 7, or T is absent, then all temporal
           methods are included. If T is absent, there should be a non-digit
           character, e.g. an asterisk, following at least a blank after
           entry M.
         * If 1 < T < 7, then T is one or is the sum of two of the following:
           1 (Pollak method), 2 (Nei/Tajima method), 4 (Jorde/Ryman method).
           The temporal method(s) to run will be the ones that make up T.
           This is similar to how M is designated.
           (If M < 8, i.e., no temporal methods, then T is ignored.)

Line 2:  A number C for the number of POSITIVE critical values. If C > 0, the
         next line should list all C critical values. If C = 0, there should
         be no line for critical values. (Molecular Coancestry method will
         ignore all positive critical values. But even if M = 4 on line 1,
         i.e., only Molecular Coancestry being run, the list of critical
         values must be entered on the next line if C > 0 is entered here.)

Line 3:  Lists all positive critical values as said on line 2.
         This line exists only if entry C on line 2 is positive.
         Critical value 0 will be automatically added to the list.
         To exclude value 0, enter "-1" after the last critical value.
         If -1 is inserted after any value listed here, the list will stop
         at that value, regardless of the value of C.
         Examples. Suppose C = 3.
         * If line 3 consists of
        	0.05  0.02  0.01
           then list of critical values is 0.05, 0.02, 0.01, and 0.
         * If line 3 consists of
        	0.05  0.02  0.01 -1
           then list of critical values is 0.05, 0.02, 0.01 (no zero).
         * If line 3 consists of
        	0.05  -1  0.02  0.01
           then list of critical values is 0.05 (no zero).
         * If line 3 consists of
        	-1  0.05  0.02  0.01
           then the list of critical values consists of ONLY 0, the effect is
           the same as C = 0.

Line 4:  For "Generation Set" in Temporal methods when M on line 1 is
         at least 8. (This line exists only if temporal is included.)
         A generation set consists of a number N followed by
         at least two ascending numbers for generations (these numbers can
         have decimals). The generation set applies to the whole input file.
         If N = 0, temporal method(s) will assume Plan II.
         If N > 0, then temporal method(s) will assume Plan I and N is
         the census population size.

Line 5:  A number M+ to indicate if extra ouput files in tabular format will
         be written for any or all methods indicated on line 1.
         The value of M+ is constructed in the same way as M on line 1.
         If M+ = 0, no extra outputs will be written.

         * Note: If M+ indicates a method not included by M, that method will
         be ignored. For example, if M = 5 (LD and Molecular Coancestry), and
         M+ = 2 (Het-Excess), then no method will have extra output file,
         the effect is the same as M+ = 0. Essentially, anything to be put
         in extra files must be included in the main output file.

         * If M+ includes temporal methods, then a second number T+ can be
         entered to indicate which temporal method(s) to be outputted in
         extra file. This T+ is interpreted the same way as T on line 1.
         Therefore, if T+ = 0, or is absent, all temporal methods for main
         output file will be in extra output file as well.
         
         However, if this T+ conflicts with T on line 1, in the sense that
         none of the methods it indicates is in the main output file, then
         the value of T+ will be ignored (as it is not entered or it is 0).
         
         For example, if M+ = M = 8, and T = 3 (Pollak and Nei/Tajima in the
         main output), but T+ = 4 (Jorde/Ryman), then this T+ conflicts with
         T, so will be ignored. As a result, Pollak and Nei/Tajima methods
         being in main output file will also be in extra output file.
         With the same example, but now T+ = 5 (Pollak and Jorde/Ryman), then
         it is not considered a conflict with T since it has Pollak method
         in common; so only Pollak method is in extra output file.

         * A third number C+ is entered for limitation on critical values
         outputted to all extra output files. To be a third, there must be a
         second on the line, which is T+, even no temporal output (T+ is
         then ignored but must be entered, such as T+ = 0).
         The number C+ is for the number of highest critical values outputted
         to extra files.
         For example, if positive critical values are 0.05, 0.02 (C = 2), and
         C+ = 1, then only critical value 0.05 is on all extra output files.

         If C+ = 0, only critical value 0 is on the extra output files.
         If C+ > C (number of POSITIVE critical values), or C+ is ABSENT,
         then all critical values, including 0, will be on extra output files.
         
         * A fourth number F can be entered for format of these tabular output
         files. If F is positive (e.g. F = 1), then a tab delimiter will
         separate any pair of outputted values. Under this format, the files
         will occupy a larger number of columns in a text editor, but when
         the files are pasted into an Excel sheet, values will be separated
         into distinct columns. If F = 0, then output files will occupy less
         columns and have a better look with a text editor.
         
         The default is F = 0, i.e., without this entry, format for these
         output files will have NO tab delimiter.
         --------------------------------------------------------------------

         The following are samples of line 5 and their meanings.
         Note that except the first entry, the default values for others are:
         	Second entry = 0,	(all temporal methods)
         	Third entry = 10,	(all critical values)
         	Fourth entry = 0.	(No tab-delimiter in the format)
         Examples:
         --------
         (1) 11
             Only one entry 11 = 1(LD) + 2(Ht) + 8(Tp). Then LD, Het-Excess,
             and all temporal methods as specified on line 1, for all critical
             values, are outputted in tabular-format output files,
             without Tab-delimiter in the format.

         (2) 11  1
             Second entry = 1, so only outputs for Pollak method will be in
             tabular-format output file - still all critical values, and no
             Tab-delimiter in the format.

         (3) 11  0  1
             Second entry = 0, all temporal methods as specified on line 1
             will be in tabular-format output file. Third entry = 1: only the
             top 1 critical value is in this output file, but still no
             Tab-delimiter in the format.

         (4) 11  0  1  1
             Fourth entry = 1: Tab-delimiter in the format.

         NAMES for EXTRA OUTPUT Files
         ----------------------------
         From the name of the main output file, the extension is removed to
         obtain the principal name, Then the following suffixes are added to
         the principal name to make the names for extra output files:

         * For LD, suffix = "xLD.txt"
         * For Het-Excess, suffix = "xHt.txt"
         * For Molecular Coancestry, suffix = "xCn.txt"
         * For Temporal, suffix = "xTp.txt"

         Examples: (All names are enclosed by double quotes.)
         (a) Suppose the main output is "main.out" or "main" (no extension).
             Then the principal name is "main"; so
               * Extra output file name for LD: "mainxLD.txt"
               * Extra output file name for Het-Excess: "mainxHt.txt"
               * Extra output file name for Molecular Coan.: "mainxCn.txt"
               * Extra output file name for Temporal: "mainxTp.txt"

         (b) Suppose the main output is "main.txt.out". Then the extension is
             "out", the principal name is "main.txt". So
               * Extra output file name for LD: "main.txtxLD.txt"
               * Extra output file name for Het-Excess: "main.txtxHt.txt"
               * Extra output file name for Molecular Coan: "main.txtxCn.txt"
               * Extra output file name for Temporal: "main.txtxTp.txt"

Line 6:  Enter 1 if confidence intervals are desired (both parametric and
         non-parametric when applicable); 0 otherwise.

Line 7:  Mating model for LD: enter 0 for Random, 1 for Monogamy.
         This line must exist if LD is to be run, i.e.,
         when entry M on line 1 is an odd number
         This line must be omitted if no LD to be run (M is even).

Line 8:  A number S for the maximum number of individuals in each population
         to be processed, starting from the first individual.
         If S = 0, no restriction.

Line 9:  Either one number P or two numbers P, Q are entered to restrict
         the processing of populations in all input files.
         If P = 0: no restriction (Q if entered will be ignored).
         If P > 0 and no Q entered, then populations up to population P will
         be processed.
         If both P and Q are entered (they should be positive) and P <= Q,
         then populations to be processed will be in the range from P to Q.
         However, if P > Q, the second entry Q is erroneous, and is rejected,
         therefore, it is assumed only one entry P is entered.

         Note that when temporal is in place, then generation set should be
         applied starting from the first population in the range.

Line 10: Enter ranges of loci in pairs; each pair must be in ascending order,
         representing one range. For examples,
              2  7   10  10   30  45
         are 3 ranges of loci: [2, 7], [10, 10], and [30, 45].
         Thus, only loci from 2 to 7 (6 loci), locus 10,  and loci from 30 to
         45 (16 loci) will be processed (total 23 loci).
         If a pair contains a zero or its two members are not in ascending
         order, then all entries from that pair and beyond will be ignored.
         In particular, if 0 is the first entry, then all entries will be
         ignored, so there will be no restriction.
         It is okay for the ranges to overlap, e.g.,
              2  5    3  10
         (Here, we have two ranges: [2, 5] and [3, 10] overlap each other.)
         If an odd number of entries are on this line, then the last entry,
         which is not paired with any, will be ignored.

Line 11: Name of main output file. This name will be used for naming extra
         output files as described for line 5 above.
         In general, all output files if existed will be overwritten starting
         with outputs for the first input file (then appended for subsequent
         input files).
         If output files need to be appended beginning with outputs for the
         first input file, then an asterisk should immediately follows the
         name of main output file (no white space in between).

Line 12 and beyond are for list of input file names, one name per line,
         the name can be terminated by an asterisk.
         If any file is not in the same directory of the executable Ne2,
         its full path name should be given.

         An empty line or a line having an asterisk as the leading character
         will terminate the list.
